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Code/PostProcessing/ABCD_vol2surf.sh

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+#!/bin/bash
+
+module load afni
+module load freesurfer
+module load fsl
+module load afni
+module load rstudio
+
+
+subject=$1
+dataDir=$2
+
+echo 'working on ' $subject
+assessment='ses-baseline-year1'
+basedir=${dataDir}/${subject}/${assessment}
+surfdir=${basedir}/surfaces/${subject}/
+vol2surf=${basedir}/surfaces/vol2surf_DWI
+tmpDIR=${basedir}/TempDir/
+dwiDIR=${basedir}/dMRI/dMRI_img//
+noddiDIR=${basedir}/dMRI/AMICO/NODDI/
+parDIR=${surfdir}/parcellation/
+
+parcellation=HCP.fsaverage.aparc
+SUBJECTS_DIR=${basedir}/surfaces/
+
+
+
+if [ -f ${basedir}/dMRI/*.nii ]; then
+	path_dwi="$(ls ${basedir}/dMRI/*.nii)"
+	gzip ${basedir}
+	path_dwi=${basedir}.gz
+elif [ -f ${basedir}/dMRI/*.nii.gz ]; then
+	path_dwi="$(ls ${basedir}/dMRI/*.nii.gz)"
+else
+	path_dwi=${basedir}.gz
+fi
+
+echo "Checking:  $vol2surf/parcellations/${parcellation}/dti_FA_rh.txt"
+if [ ! -f $vol2surf/parcellations/${parcellation}/dti_FA_rh.txt ]; then
+
+if [ ! -f ${surfdir}/mri/T1.nii ]; then
+echo 'Converting'
+	mri_convert -i ${surfdir}/mri/T1.mgz -o ${surfdir}/mri/T1.nii
+fi
+
+
+if [ ! -f "$vol2surf"/bbregister/DWI_to_T1.lta ]; then
+	mkdir -p "$vol2surf"/bbregister/
+	bbregister --s "$subject" --mov $path_dwi --reg "$vol2surf"/bbregister/DWI_to_T1.lta --init-fsl --dti
+fi
+
+
+#ConvertSurface -i_gii ${vol2surf}/NODDI_ICVF_lh_al2surf.func.gii -o_fs ${vol2surf}/NODDI_ICVF_lh_al2surf.func.pial
+
+cd ${surfdir}
+echo "Checking SUMA"
+if [ ! -f  ${surfdir}/SUMA/std.60.rh.thickness.niml.dset ]; then
+	echo "running SUMA"
+	rm -r /SUMA/
+	@SUMA_Make_Spec_FS -NIFTI -sid ${subject} -fs_setup
+	gzip *.nii
+fi
+
+
+#declare -a files=("NODDI_ISOVF" "NODDI_ICVF" "NODDI_OD" "dti_MD" "dti_FA")
+declare -a files=("FIT_ICVF" "FIT_OD" "FIT_ISOVF" "dti_MD" "dti_FA")
+
+
+for hemi in lh rh; do
+	[[ $hemi == lh ]] && hemisphere=l || hemisphere=r
+	if [ ! -f ${vol2surf}/${hemi}_thickness_std60.func.gii ]; then
+		ConvertDset -o_gii -input ${surfdir}/SUMA/std.60.${hemi}.thickness.niml.dset -prefix ${vol2surf}/${hemi}_thickness_std60.func.gii
+	fi
+
+
+	for file in ${files[@]}; do
+echo "checking vol2vol"
+	if  [ ! -f $vol2surf/${file}_T1space.nii.gz ]; then
+
+		if [ -f $dwiDIR/${file}.nii.gz ]; then
+			p_file=$dwiDIR/${file}.nii.gz
+		elif [ -f $noddiDIR/${file}.nii.gz ]; then
+			p_file=$noddiDIR/${file}.nii.gz
+		else
+			echo "ERROR file not found:  $dwiDIR/${file}.nii.gz "
+		fi		
+		mri_vol2vol  	--reg "$vol2surf"/bbregister/DWI_to_T1.lta \
+				--mov ${p_file} \
+				--fstarg \
+				--o $vol2surf/${file}_T1space.nii.gz 
+	fi
+
+echo "Checking $vol2surf/${file}_T1space_al2std60_${hemi}.func.gii "
+	if [ ! -f  $vol2surf/${file}_T1space_al2std60_${hemi}.func.gii ]; then
+
+		wb_command -volume-to-surface-mapping $vol2surf/${file}_T1space.nii.gz ${surfdir}/SUMA/std.60.${hemi}.pial.gii $vol2surf/${file}_T1space_al2std60_${hemi}.func.gii -myelin-style ${surfdir}/SUMA/${hemi}.ribbon.nii.gz ${vol2surf}/${hemi}_thickness_std60.func.gii 5
+	fi
+
+
+	if [ ! -f $vol2surf/${file}_T1space_al2std60_${hemi}.txt ]; then
+		echo "Running WB_surf2table"
+		Rscript /rds/project/rb643-1/rds-rb643-ukbiobank2/Code/WB_surf2table_giii.r $vol2surf/${file}_T1space_al2std60_${hemi}.func.gii $vol2surf/${file}_T1space_al2std60_${hemi}.txt
+	fi
+
+	if [ ! -f $vol2surf/surface/${file}_T1space_al2std60_back2sub_${hemi}.1D ]; then
+		SurfToSurf -i_gii ${surfdir}/SUMA/${hemi}.sphere.gii -i_gii  ${surfdir}/SUMA/std.60.${hemi}.sphere.gii -data $vol2surf/${file}_T1space_al2std60_${hemi}.txt -prefix $vol2surf/${file}_T1space_al2std60_back2sub_${hemi}
+		mkdir $vol2surf/surface/
+		mv $vol2surf/${file}_T1space_al2std60_back2sub_${hemi}.1D  $vol2surf/surface/${file}_T1space_al2std60_back2sub_${hemi}.1D 	
+	fi
+
+	mkdir -p $vol2surf/parcellations/${parcellation}/
+
+	if [ ! -f $vol2surf/parcellations/${parcellation}/${file}_${hemi}.txt ]; then
+		Rscript /rds/project/rb643-1/rds-rb643-ukbiobank2/Code/WB_annot2table.r ${surfdir}/label/${hemi}.${parcellation}.annot $vol2surf/surface/${file}_T1space_al2std60_back2sub_${hemi}.1D $vol2surf/parcellations/${parcellation}/${file}_${hemi}.txt
+	fi
+
+	done
+
+done
+	rm -r ${surfdir}/SUMA/
+	rm ${surfdir}/mri/orig/COR*
+	find $vol2surf/ -maxdepth 1 -type f -delete
+	rm ${surfdir}/surf/*.asc
+fi